On evolutionary time scales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographical dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutli-locus data set that included ten species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed: A. sexfasciatus and A. vaigiensis. The results showed three regional sub-lineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis is polyphyletic and consists of three distinct genetic lineages (A, B, and C) whose geographic ranges overlap (9% divergence at cytb). Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. These fishes may be considered as candidates of choice to investigate the complexity of the discrepancies between phenotypic and genetic evolution among sibling species.